Merge pull request #1 from TissueImageAnalytics/develop

Merge develop

Author: mbasheer04

.github/workflows/conda-env-create.yml

@@ -40,7 +40,7 @@ jobs:
           cp ./requirements/requirements*.txt /tmp/
           mkdir /tmp/docs/
           cp ./docs/requirements*.txt /tmp/docs/
-      - uses: mamba-org/provision-with-micromamba@main
+      - uses: mamba-org/setup-micromamba@v1
         with:
           environment-name: tiatoolbox
           environment-file: ${{ matrix.requirements }}

.github/workflows/docker-publish.yml

@@ -6,7 +6,7 @@ env:
   REGISTRY: ghcr.io
   IMAGE_NAME: TissueImageAnalytics/tiatoolbox
   image: ghcr.io/tissueimageanalytics/tiatoolbox
-  TOOLBOX_VER: 1.5.1
+  TOOLBOX_VER: 1.6.0
 
 jobs:
   build-and-push-image:

.github/workflows/python-package.yml

@@ -30,7 +30,7 @@ jobs:
         sudo apt update
         sudo apt-get install -y libopenslide-dev openslide-tools libopenjp2-7 libopenjp2-tools
         python -m pip install --upgrade pip
-        python -m pip install ruff==0.7.4 pytest pytest-cov pytest-runner
+        python -m pip install ruff==0.8.2 pytest pytest-cov pytest-runner
         pip install -r requirements/requirements.txt
     - name: Cache tiatoolbox static assets
       uses: actions/cache@v3

.gitignore

@@ -116,3 +116,6 @@ ENV/
 
 # vim/vi generated
 *.swp
+
+# output zarr generated
+*.zarr

.pre-commit-config.yaml

@@ -23,7 +23,7 @@ repos:
         - mdformat-black
         - mdformat-myst
   - repo: https://github.com/executablebooks/mdformat
-    rev: 0.7.18
+    rev: 0.7.21
     hooks:
     - id: mdformat
       # Optionally add plugins
@@ -60,7 +60,7 @@ repos:
       - id: rst-inline-touching-normal # Detect mistake of inline code touching normal text in rst.
   - repo: https://github.com/astral-sh/ruff-pre-commit
     # Ruff version.
-    rev: v0.7.4
+    rev: v0.8.6
     hooks:
       - id: ruff
         args: [--fix, --exit-non-zero-on-fix]

AUTHORS.md

@@ -11,18 +11,19 @@
 - Mostafa Jahanifar \<@mostafajahanifar>
 - David Epstein \<@DavidBAEpstein>
 - Adam Shephard \<@adamshephard>
-- Ruqayya Awan \<@ruqayya>
 - Abdullah Alsalemi \<@Abdol>
+- Ruqayya Awan \<@ruqayya>
+- Jiaqi Lv \<@Jiaqi-Lv>
 - Dmitrii Blaginin \<@blaginin>
 - Srijay Deshpande \<@Srijay-lab>
-- Jiaqi Lv\<@Jiaqi-Lv>
 - George Hadjigeorgiou \<@ghadjigeorghiou>
 - Abishekraj Vinayagar Gnanasambandam \<@AbishekRajVG>
 - Wenqi Lu \<@wenqi006>
 - Saad Bashir \<@rajasaad>
 
 ## Contributors
 
+- George Batchkala \<@GeorgeBatch>
 - Rob Jewsbury \<@R-J96>
 - Mohsin Bilal \<@mbhahsmi>
 - Fayyaz Minhas \<@foxtrotmike>

CITATION.cff

@@ -44,7 +44,7 @@ authors:
   given-names: "Shan E Ahmed"
   orcid: "https://orcid.org/0000-0002-1097-1738"
 title: "TIAToolbox as an end-to-end library for advanced tissue image analytics"
-version: 1.5.1  # TIAToolbox version
+version: 1.6.0  # TIAToolbox version
 doi: 10.5281/zenodo.5802442
 date-released: 2022-10-20
 url: "https://github.com/TissueImageAnalytics/tiatoolbox"